Hi,
I'm trying to run qiime2 on a HPC cluster but I'm running into a permission error in my home directory. I contacted the administrator and he recommended that I redirect the location of .config to the /share folder in which I'm executing the slurm command (/share/taglab/Erol/). How can I do this?
This is the slurm script that I'm running in /share/taglab/Erol/ (not /home/eskavvas/)
#!/bin/bash
#SBATCH --job-name=denoise
#SBATCH --nodes=1
#SBATCH --ntasks=64
#SBATCH --time=12:00:00
#SBATCH --mem=50G
#SBATCH --partition=production
#SBATCH --output=stdout_%j.out
#SBATCH --error=stderr_%j.err
#SBATCH --array=1-15 # this specifies the number of jobs to run in array.. corresponds to the files in my directory
module load anaconda3/4.8.3
module load qiime2/2020.8
source activate qiime2-2020.8
echo "My SLURM_ARRAY_TASK_ID: " $SLURM_ARRAY_TASK_ID
name=`sed "${SLURM_ARRAY_TASK_ID}q;d" samples.txt`
echo $name
qiime dada2 denoise-single \
--i-demultiplexed-seqs ./demux_seqs_fd_$name.qza \
--p-trunc-len 150 \
--p-n-threads 0 \
--o-table ./dada2_table_fd_$name.qza \
--o-representative-sequences ./dada2_rep_set_fd_$name.qza \
--o-denoising-stats ./dada2_stats_fd_$name.qza
echo denoising done!
This is the resulting error.
Traceback (most recent call last):
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/bin/qiime", line 11, in
sys.exit(qiime())
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1254, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1297, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 100, in get_command
plugin = self._plugin_lookup[name]
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in
CACHE = DeploymentCache()
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 58, in init
self._cache_dir = self._get_cache_dir()
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 85, in _get_cache_dir
os.makedirs(cache_dir, exist_ok=True)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/os.py", line 210, in makedirs
makedirs(head, mode, exist_ok)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/os.py", line 210, in makedirs
makedirs(head, mode, exist_ok)
File "/software/qiime2/2020.8/lssc0-linux/miniconda3/envs/qiime2-2020.8/lib/python3.6/os.py", line 220, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/home/eskavvas/.config'
I was looking on the forum it seems like a similar issue comes up with using dockers, but I'm not sure how to fix it in this case.
I appreciate any help, thanks!
Erol